FMO DATABASE

FMODB ID: KGM63

Calculation Name: 4C0H-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C0H

Chain ID: C

ChEMBL ID:

UniProt ID: Q08685

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	28
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-83483.313215
FMO2-HF: Nuclear repulsion	71953.040899
FMO2-HF: Total energy	-11530.272316
FMO2-MP2: Total energy	-11564.224408

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(C:464:SER)

Summations of interaction energy for fragment #1(C:464:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-2.611	-1.1	-0.021	-0.797	-0.693	0.002

Interaction energy analysis for fragmet #1(C:464:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.026

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	C	466	SER	0	0.035	-0.009	3.778	-2.628	-1.117	-0.021	-0.797	-0.693	0.002
4	C	467	ASN	0	-0.004	-0.002	5.892	0.003	0.003	0.000	0.000	0.000	0.000
5	C	476	ASN	0	-0.002	-0.012	19.619	0.006	0.006	0.000	0.000	0.000	0.000
6	C	477	ILE	0	-0.004	0.004	15.165	-0.006	-0.006	0.000	0.000	0.000	0.000
7	C	478	GLN	0	0.020	0.008	17.796	0.027	0.027	0.000	0.000	0.000	0.000
8	C	479	SER	0	-0.033	-0.024	16.065	-0.011	-0.011	0.000	0.000	0.000	0.000
9	C	480	ARG	1	0.950	0.989	17.355	-0.028	-0.028	0.000	0.000	0.000	0.000
10	C	481	ASN	0	0.041	0.019	19.262	0.006	0.006	0.000	0.000	0.000	0.000
11	C	482	TRP	0	-0.005	-0.009	17.142	0.013	0.013	0.000	0.000	0.000	0.000
12	C	483	TYR	0	-0.003	0.000	22.705	-0.014	-0.014	0.000	0.000	0.000	0.000
13	C	484	LEU	0	0.014	0.019	25.882	0.002	0.002	0.000	0.000	0.000	0.000
14	C	485	SER	0	0.001	-0.001	29.205	0.003	0.003	0.000	0.000	0.000	0.000
15	C	486	ASP	-1	-0.835	-0.930	30.944	0.046	0.046	0.000	0.000	0.000	0.000
16	C	487	SER	0	-0.031	-0.027	34.194	-0.003	-0.003	0.000	0.000	0.000	0.000
17	C	488	GLN	0	-0.035	-0.024	30.919	0.000	0.000	0.000	0.000	0.000	0.000
18	C	489	TRP	0	0.024	0.012	32.061	-0.003	-0.003	0.000	0.000	0.000	0.000
19	C	490	ALA	0	0.004	0.011	34.278	-0.003	-0.003	0.000	0.000	0.000	0.000
20	C	491	ALA	0	-0.069	-0.037	37.608	-0.003	-0.003	0.000	0.000	0.000	0.000
21	C	492	PHE	0	-0.014	0.006	32.703	-0.002	-0.002	0.000	0.000	0.000	0.000
22	C	493	LYS	1	0.906	0.957	36.897	-0.009	-0.009	0.000	0.000	0.000	0.000
23	C	494	ASP	-1	-0.831	-0.937	34.827	0.007	0.007	0.000	0.000	0.000	0.000
24	C	495	ASP	-1	-0.961	-0.972	36.120	-0.007	-0.007	0.000	0.000	0.000	0.000
25	C	496	GLU	-1	-0.976	-0.989	34.792	0.001	0.001	0.000	0.000	0.000	0.000
26	C	497	ILE	0	-0.072	-0.023	30.953	-0.003	-0.003	0.000	0.000	0.000	0.000
27	C	498	THR	0	-0.060	-0.026	33.432	-0.004	-0.004	0.000	0.000	0.000	0.000
28	C	499	SER	0	-0.030	-0.010	35.457	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:464:SER)